The visitors started brightly but struggled to create any clear-cut openings against an Iron defence that has now kept 21 clean sheets this season.
United began to take control towards the end of the first half with on-loan striker Jermaine Beckford twice going close.
First he volleyed a difficult chance just over before being denied by the fingertips of goalkeeper Steve Mildenhall.
It was during a period of fierce Scunthorpe pressure that Jones turned a left-wing cross from Kevan Hurst into his own net.
Scunthorpe should have wrapped the game up in the 61st minute when leading marksman Billy Sharp burst free through the middle and looked set for his 28th goal of the season.
But he was denied by a good save from Mildenhall that kept Yeovil in the game.
The visitors nearly snatched an equaliser in the 79th minute with their best chance of the match when Wayne Gray headed just wide at the near post from Chris Cohen's left-wing cross.